Contacts of the strand formed by residues 75 - 89 (chain B) in PDB entry 3M4D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLU* 3.8 0.5 - - - -
71B GLU* 3.1 68.6 + - + +
72B GLY 3.4 8.1 - - - +
74B ASN* 1.3 83.6 - - + +
76B SER* 1.3 70.8 + - - +
206B ALA* 3.5 3.9 - - - +
257B GLN* 3.3 26.6 + - + +
258B LEU 3.3 9.6 - - - +
259B HIS* 4.6 10.5 - - + -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 3.2 17.8 - - - +
69B SER* 2.8 24.4 + - - -
70B GLU* 4.3 2.4 - - - +
71B GLU* 6.3 0.4 - - - -
75B LYS* 1.3 80.8 - - - +
77B GLY* 1.3 60.0 + - - +
206B ALA* 3.7 6.3 - - - +
207B ALA* 3.4 31.9 - - - +
210B PHE* 3.5 8.2 - - - -
257B GLN* 3.4 7.1 - - - +
258B LEU 3.1 29.8 + - - +
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 3.2 10.4 - - - +
68B TYR* 3.0 44.7 + - - -
69B SER* 3.1 14.5 + - - -
76B SER* 1.3 78.0 + - - +
78B LEU* 1.3 58.8 + - - -
210B PHE* 3.8 3.6 - - - -
256B TYR 3.6 5.4 - - - -
257B GLN* 4.2 4.7 - - - -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B TYR* 3.4 46.4 - - + +
66B ARG* 3.3 39.5 - - - +
67B VAL* 3.7 8.1 - - + +
68B TYR* 3.4 4.8 - - - -
77B GLY* 1.3 73.9 - - - +
79B ALA* 1.3 63.7 + - - +
80B TRP* 3.9 1.4 + - + -
196B PHE* 3.9 19.3 - - + -
210B PHE* 3.7 29.2 - - + -
254B ASP 3.7 0.5 - - - +
255B ASP* 3.7 2.1 - - - -
256B TYR* 2.7 47.4 + - + +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN 3.5 5.4 - - - +
65B TYR* 3.4 4.5 - - - -
66B ARG* 2.9 37.0 + - + +
68B TYR* 3.7 12.9 - - + -
78B LEU* 1.3 74.0 - - - +
80B TRP* 1.3 59.2 + - - +
253B ARG* 3.9 22.2 - - - +
254B ASP 3.4 6.1 - - - -
274B TRP* 3.4 26.0 - - + -
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Residues in contact with TRP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN 5.1 0.2 - - - -
65B TYR* 3.9 20.9 - - + +
78B LEU* 3.9 4.3 - - + -
79B ALA* 1.3 75.8 - - - +
81B PRO* 1.3 89.0 - - + +
82B SER* 3.3 13.2 + - - -
171B PHE* 3.5 34.3 - + - -
184B ARG* 3.6 28.7 - - + -
195B LEU* 3.8 15.0 - - + -
196B PHE* 3.4 22.5 - + + -
220B LEU* 3.8 10.8 - - + -
253B ARG* 3.0 7.8 - - - +
254B ASP* 2.7 66.9 + - + +
256B TYR* 3.8 16.1 - - + +
269B ASN* 3.0 24.3 + - - -
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Residues in contact with PRO 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 3.4 20.0 - - - +
65B TYR 4.4 1.8 - - - +
80B TRP* 1.3 96.2 - - + +
82B SER* 1.3 61.5 - - - +
83B ALA 3.3 2.0 - - - +
84B PHE* 3.7 26.0 - - + -
153B PHE* 3.8 8.4 - - - -
220B LEU* 3.3 49.6 - - + +
251B ARG* 4.0 13.7 - - + -
252B VAL 3.4 7.4 - - - +
253B ARG* 4.2 2.4 - - + -
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B TRP* 3.3 20.6 + - - -
81B PRO* 1.3 72.4 - - - +
83B ALA* 1.3 62.4 + - - +
153B PHE* 4.5 1.1 - - - -
170B ILE* 3.6 2.4 - - - +
171B PHE* 2.9 27.5 + - - +
184B ARG* 3.5 18.8 + - - -
252B VAL* 2.8 23.8 + - - +
254B ASP* 2.7 38.0 + - - -
272B ASP* 3.8 0.5 + - - -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PRO* 3.3 2.3 + - - +
82B SER* 1.3 85.0 - - - +
84B PHE* 1.3 68.4 + - - +
85B LYS* 4.7 10.8 - - - -
153B PHE* 4.8 0.2 - - - -
169B VAL 3.3 10.1 - - - +
170B ILE* 4.1 16.2 - - + -
251B ARG* 3.5 4.9 - - - +
252B VAL* 2.9 48.5 + - + +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE* 3.6 47.8 - - + -
62B ALA 3.9 8.1 - - - -
81B PRO* 3.7 22.7 - - + -
83B ALA* 1.3 77.8 - - - +
85B LYS* 1.3 62.3 + - - +
153B PHE* 3.9 23.8 - + - -
168B LYS* 3.3 2.6 - - - -
169B VAL* 2.7 48.0 + - + +
219B LEU* 3.2 31.4 - - + -
224B PHE* 3.9 39.5 - + + -
250B GLU 3.4 5.8 - - - +
251B ARG* 4.6 2.2 - - + -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 4.0 1.9 - - - +
83B ALA* 4.7 9.4 - - + -
84B PHE* 1.3 82.9 - - - +
86B VAL* 1.3 68.4 + - - +
87B GLN* 4.3 18.2 - - + +
158B GLU* 4.3 15.2 + - - +
167B TRP 3.3 7.9 - - - +
168B LYS* 3.8 27.4 - - + +
170B ILE* 5.7 0.4 - - - -
228B PHE* 6.1 0.4 - - - -
248B ILE 4.3 0.7 - - - -
249B TYR* 3.4 1.6 - - - -
250B GLU* 2.8 69.9 + - + +
252B VAL* 4.6 13.4 - - + +
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B THR* 3.6 34.3 - - + +
61B ILE* 4.7 1.8 - - + -
85B LYS* 1.3 80.7 - - - +
87B GLN* 1.3 65.8 + - - +
88B LEU* 4.3 7.9 - - + -
166B GLY* 3.2 2.6 - - - -
167B TRP* 2.9 32.9 + - + -
224B PHE* 5.5 1.3 - - + -
226B PRO* 3.7 31.4 - - + -
228B PHE* 3.8 20.6 - - + -
248B ILE 3.2 4.5 - - - +
249B TYR* 4.0 22.4 - - + -
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Residues in contact with GLN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LYS* 4.3 18.9 - - + +
86B VAL* 1.3 84.3 - - - +
88B LEU* 1.3 67.7 + - - +
89B GLN* 6.4 0.2 - - + -
158B GLU* 3.0 31.5 + - - +
165B VAL 3.5 9.6 - - - +
166B GLY* 4.4 0.4 - - - -
246B ASP 3.8 0.4 - - - +
247B VAL* 3.2 5.5 - - - +
248B ILE* 2.8 55.0 + - + +
250B GLU* 5.0 3.1 + - - +
277B ARG* 3.8 21.7 + - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ILE* 4.0 23.3 - - + -
57B THR* 4.1 15.5 - - + -
86B VAL* 4.3 4.3 - - + -
87B GLN* 1.3 83.7 - - - +
89B GLN* 1.3 63.1 + - - +
98B ILE* 5.5 1.3 - - + -
163B LYS 4.6 0.2 - - - -
164B LYS* 3.3 4.5 - - - +
165B VAL* 2.9 42.8 + - + +
167B TRP* 4.0 17.9 - - + -
230B THR* 3.8 29.4 - - + +
245B ILE* 4.0 23.1 - - + -
246B ASP 3.2 4.9 - - - +
247B VAL* 3.8 20.9 - - + -
248B ILE* 5.8 0.4 - - - -
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLN* 6.4 0.4 - - + -
88B LEU* 1.3 77.9 - - - +
90B LEU* 1.3 78.2 + - - +
91B PRO* 3.8 3.7 - - + +
92B ASP* 4.6 10.4 - - - +
98B ILE* 6.0 0.2 - - - -
163B LYS* 3.3 11.2 - - + +
164B LYS* 4.1 23.9 - - + +
245B ILE* 3.6 4.2 - - - +
246B ASP* 2.9 44.0 + - + +
248B ILE* 5.7 5.1 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il